Although the exact origin of this classic cocktail is subject of numerous debates, Cuba is the birthplace of Mojito. One story traces the cocktail to a similar 16th century drink, named “El Draque”, in honor of Sir Francis Drake. It was made initially with tafia/aguardiente, a primitive predecessor of rum, but rum was used as soon as it became widely available. Mint, lime and sugar were also helpful in hiding the harsh taste of this spirit. While this drink was not called Mojito at this time, it was still the original combination of these ingredients.

Some historians contend that African slaves that worked in the Cuban sugar cane fields during the 19th century were instrumental in the cocktail's origin. Guarapo, the sugar cane juice often used in Mojitos, was a popular drink amongst the slaves who helped coin the name of the sweet nectar.

There are several theories behind the origin of the name Mojito: one such theory holds that name relates to mojo, a Cuban seasoning made from lime and used to flavour dishes, but another theory is that the name Mojito is simply a derivative of mojadito, Spanish for "a little wet", or simply the diminutive of "mojado" (which means wet).